Eating and cooking qualities (ECQs) of rice (Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. The starch physicochemical properties, i.e. amylose content, gel consistency, gelatinization temperature and pasting viscosity are important indices for evaluating rice ECQs. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors. A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All traits showed a large phenotypic variation and highly significant phenotypic correlations were present between most of traits. A total of 33 and 30 loci were located for 11 ECQs in indica and japonica subpopulations respectively. Most of associated loci were overlapped with starch synthesis-related genes (SSRGs), and the Wx locus gathered 14 associated loci with the largest effects on amylose content, gel consistency and pasting viscosities. Eight subpopulation specific markers, RM588, Wx-(CT)n, SSI and SBE1 for indica subpopulation and RM550, Wxmp, SSIIa and SBE4 for japonica subpopulation, were identified, suggesting alleles of SSRGs showed the subspecific tendency. Nevertheless, allelic variation in SSIIa showed no tendency towards subspecies. One associated maker RM550 detected in japonica subpopulation for amylose content and pasting viscosity was verified a potential novel and stably expressed locus and could be selected for further fine mapping. This study illustrated the potential for dissecting genetic factors of complex traits in domesticated rice subspecies and provided highly associated markers to facilitate marker-assisted selection for breeding high-quality indica or japonica rice varieties.

中文翻译：

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通过关联图谱分析不同栽培稻（Oryza sativa L.）不同亚群饮食和烹饪品质的遗传

稻米（Oryza sativa L.）的饮食质量（ECQs）决定了消费者对稻米品种的接受程度以及其经济价值。淀粉的理化特性，即直链淀粉含量，凝胶稠度，糊化温度和糊化粘度是评估稻米ECQ的重要指标。遗传因素是具有优异ECQs的水稻品种发展所必需的，并且关联图谱是发现此类关联遗传因素的有前途的方法之一。通过连续两年对11种ECQ性状进行表型分析，并使用210种多态SSR和候选基因标记进行基因分型，对253种非糯稻材料（包括83个in稻和170个粳稻栽培的水稻品种）进行了全基因组关联映射。这些标记平均扩增了747个等位基因3。每个位点57个等位基因。结构，系统发育关系和主成分分析表明，and稻和粳稻种之间有很强的群体分化，因此在in稻和粳稻亚群内进行了关联作图。所有性状均表现出较大的表型变异，并且大多数性状之间存在高度显着的表型相关性。分别在in种和粳稻亚群中分别为11个ECQs定位了33个和30个基因座。大多数相关基因座都与淀粉合成相关基因（SSRGs）重叠，并且Wx基因座收集了14个相关基因座，这对直链淀粉含量，凝胶稠度和糊化粘度影响最大。八种亚群特异性标记，分别为588588亚群，RM588，Wx-（CT）n，SSI和SBE1以及RM550，Wxmp 鉴定了用于粳稻亚群的SSIIa和SBE4，这表明SSRGs的等位基因表现出亚特异性趋势。尽管如此，SSIIa的等位基因变异并未显示出亚种趋势。验证了在粳稻亚群中检测到的直链淀粉含量和糊化粘度的一个相关制造商RM550，它是潜在的新颖且稳定表达的基因座，可以选择用于进一步的精细作图。这项研究阐明了在解剖的水稻亚种中分析复杂性状遗传因素的潜力，并提供了高度相关的标记，以便于标记辅助选择，以选育优质in稻或粳稻品种。验证了在粳稻亚群中检测到的直链淀粉含量和糊化粘度的一个相关制造商RM550，它是潜在的新颖且稳定表达的基因座，可以选择用于进一步的精细作图。这项研究阐明了在解剖的水稻亚种中分析复杂性状遗传因素的潜力，并提供了高度相关的标记，以便于标记辅助选择，以选育优质in稻或粳稻品种。验证了在粳稻亚群中检测到的直链淀粉含量和糊化粘度的一个相关制造商RM550，它是潜在的新颖且稳定表达的基因座，可以选择用于进一步的精细作图。这项研究阐明了在解剖的水稻亚种中分析复杂性状遗传因素的潜力，并提供了高度相关的标记，以便于标记辅助选择，以选育优质in稻或粳稻品种。